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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/seqkit">Debian Med / seqkit</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/41351e95dc3ac706e5b55e9320d3ce5a37576595">41351e95</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-07-27T02:50:24+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.16.1+ds</pre>
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<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/4bd6a740e922520d8dc9409695075cae1f6aad46">4bd6a740</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-07-27T02:50:24+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">[skip ci] Interim changelog entry
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<h4>7 changed files:</h4>
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<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#7cdca301cbb4c2d5233c0eed1f6571d394148920">
doc/docs/download.md
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<li class="file-stats">
<a href="#604fd55a896e470ee80f4ea9caf71f879579d68c">
seqkit/cmd/pair.go
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<a href="#1d415668e438829ee466a5e6b51f9c42ca064b0c">
seqkit/cmd/shuffle.go
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<li class="file-stats">
<a href="#92b5b49951aa33ccf0a6d8b10622240cc64511e8">
seqkit/cmd/sort.go
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<li class="file-stats">
<a href="#9b440ae881620aea38a06351cb2ab92f966a94f0">
seqkit/cmd/version.go
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<h4>Changes:</h4>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/seqkit/-/compare/74269afe083ed3110d498bcfc78d8652fcde30f8...4bd6a740e922520d8dc9409695075cae1f6aad46#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">SeqKit v0.16.1</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/tag/v0.16.1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Release)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/v0.16.1/total.svg</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/tag/v0.16.1)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit shuffle --two-pass`</span>: fix bug introduced in <span class="p">[</span><span class="nv" style="color: #008080;">#173</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/173</span><span class="p">)</span> . <span class="p">[</span><span class="nv" style="color: #008080;">#209</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/209</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit pair`</span>: fix a dangerous bug: when input files are not in current directory, input files were overwritten.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">SeqKit v0.16.0</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/tag/v0.16.0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Release)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/v0.16.0/total.svg</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p"> -</span> new command <span class="sb" style="color: #d14;">`seqkit head-genome`</span>:</span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/seqkit/-/compare/74269afe083ed3110d498bcfc78d8652fcde30f8...4bd6a740e922520d8dc9409695075cae1f6aad46#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">seqkit (0.16.<span class="idiff left right">0</span>+ds-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">seqkit (0.16.<span class="idiff left right">1</span>+ds-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * d/watch: Fix watch regex</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * New upstream version 0.16.0+ds</span>
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<li id="7cdca301cbb4c2d5233c0eed1f6571d394148920">
<a href="https://salsa.debian.org/med-team/seqkit/-/compare/74269afe083ed3110d498bcfc78d8652fcde30f8...4bd6a740e922520d8dc9409695075cae1f6aad46#7cdca301cbb4c2d5233c0eed1f6571d394148920"><strong>doc/docs/download.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,28 +6,10 @@ SeqKit is implemented in [Go](https://golang.org/) programming language,</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Latest Version</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">SeqKit v0.16.0</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/tag/v0.16.0</span><span class="p">)</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Release)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/v0.16.0/total.svg</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0)</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="p"> -</span> new command <span class="sb" style="color: #d14;">`seqkit head-genome`</span>:</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="p"> -</span> print sequences of the first genome with common prefixes in name</span>
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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit grep/locate/amplicon -m`</span></span>
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14
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="p"> -</span> <span class="ge" style="font-style: italic;">*much faster (300-400x) searching with mismatch allowed*</span> by optimizing FM-indexing and parallelization.</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="p"> -</span> new flag <span class="sb" style="color: #d14;">`-I/--immediate-output`</span>.</span>
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16
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit grep/locate`</span>:</span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown"><span class="p"> -</span> fix bug of <span class="sb" style="color: #d14;">`-m`</span> when querying contains letters not in alphabet, usually for protein sequences. <span class="p">[</span><span class="nv" style="color: #008080;">#178</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/178</span><span class="p">)</span>, <span class="p">[</span><span class="nv" style="color: #008080;">#179</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/179</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="p"> -</span> onply search on positive strand when searching unlimited or protein sequences.</span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit locate`</span>:</span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown"><span class="p"> -</span> removing debug info for <span class="sb" style="color: #d14;">`-r`</span> introduced in a0f6b6e. <span class="p">[</span><span class="nv" style="color: #008080;">#180</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/180</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit amplicon`</span>:</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="p"> -</span> fix bug of <span class="sb" style="color: #d14;">`-m`</span>, when mismatch is allowed.</span>
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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
23
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit fx2tab`</span>:</span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
24
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"><span class="p"> -</span> new flag <span class="sb" style="color: #d14;">`-C/--base-count`</span> for counting bases. <span class="p">[</span><span class="nv" style="color: #008080;">#183</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/183</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
25
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit tab2fx`</span>:</span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
26
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown"><span class="p"> -</span> fix a rare bug. <span class="p">[</span><span class="nv" style="color: #008080;">#197</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/197</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
27
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit subseq`</span>:</span>
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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
28
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown"><span class="p"> -</span> fix bug for BED with empty columns. <span class="p">[</span><span class="nv" style="color: #008080;">#195</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/195</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
29
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit genautocomplete`</span>: </span>
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<td class="old_line diff-line-num old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
30
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<td class="new_line diff-line-num old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="p"> -</span> <span class="gs" style="font-weight: 600;">**support bash|zsh|fish|powershell**</span>.</span>
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<td class="old_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">SeqKit v0.16.1</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/tag/v0.16.1</span><span class="p">)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Release)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/v0.16.1/total.svg</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/tag/v0.16.1)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit shuffle --two-pass`</span>: fix bug introduced in <span class="p">[</span><span class="nv" style="color: #008080;">#173</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/173</span><span class="p">)</span> . <span class="p">[</span><span class="nv" style="color: #008080;">#209</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/209</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit pair`</span>: fix a dangerous bug: when input files are not in current directory, input files were overwritten.</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Please cite</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,13 +26,13 @@ SeqKit is implemented in [Go](https://golang.org/) programming language,</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown">OS |Arch |File, 中国镜像 |Download Count</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown">:------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown">Linux |32-bit |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_linux_386.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">0</span>/seqkit_linux_386.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">0</span>/seqkit_linux_386.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown">Linux |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">0</span>/seqkit_linux_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">0</span>/seqkit_linux_amd64.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown">Linux |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">0</span>/seqkit_linux_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">0</span>/seqkit_linux_arm64.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown">macOS |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">0</span>/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">0</span>/seqkit_darwin_amd64.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown">macOS |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">0</span>/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">0</span>/seqkit_darwin_arm64.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown">Windows|32-bit |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_windows_386.exe.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">0</span>/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">0</span>/seqkit_windows_386.exe.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown">Windows|<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_windows_amd64.exe.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">0</span>/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>|<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">0</span>/seqkit_windows_amd64.exe.tar.gz)</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">Linux |32-bit |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_linux_386.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">1</span>/seqkit_linux_386.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">1</span>/seqkit_linux_386.tar.gz)</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown">Linux |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">1</span>/seqkit_linux_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">1</span>/seqkit_linux_amd64.tar.gz)</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown">Linux |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">1</span>/seqkit_linux_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">1</span>/seqkit_linux_arm64.tar.gz)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">macOS |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">1</span>/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">1</span>/seqkit_darwin_amd64.tar.gz)</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown">macOS |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">1</span>/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">1</span>/seqkit_darwin_arm64.tar.gz)</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown">Windows|32-bit |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_windows_386.exe.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">1</span>/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">1</span>/seqkit_windows_386.exe.tar.gz)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown">Windows|<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_windows_amd64.exe.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff left">1</span>/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>|<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v0.16.<span class="idiff right">1</span>/seqkit_windows_amd64.exe.tar.gz)</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"></span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,6 +110,28 @@ fish:</td>
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128
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"></span>
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129
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Release History</span></span>
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130
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">SeqKit v0.16.0</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/tag/v0.16.0</span><span class="p">)</span></span>
</pre>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Release)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/v0.16.0/total.svg</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0)</span>
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"><span class="p"> -</span> new command <span class="sb" style="color: #d14;">`seqkit head-genome`</span>:</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"><span class="p"> -</span> print sequences of the first genome with common prefixes in name</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit grep/locate/amplicon -m`</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"><span class="p"> -</span> <span class="ge" style="font-style: italic;">*much faster (300-400x) searching with mismatch allowed*</span> by optimizing FM-indexing and parallelization.</span>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"><span class="p"> -</span> new flag <span class="sb" style="color: #d14;">`-I/--immediate-output`</span>.</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit grep/locate`</span>:</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"><span class="p"> -</span> fix bug of <span class="sb" style="color: #d14;">`-m`</span> when querying contains letters not in alphabet, usually for protein sequences. <span class="p">[</span><span class="nv" style="color: #008080;">#178</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/178</span><span class="p">)</span>, <span class="p">[</span><span class="nv" style="color: #008080;">#179</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/179</span><span class="p">)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"><span class="p"> -</span> onply search on positive strand when searching unlimited or protein sequences.</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit locate`</span>:</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"><span class="p"> -</span> removing debug info for <span class="sb" style="color: #d14;">`-r`</span> introduced in a0f6b6e. <span class="p">[</span><span class="nv" style="color: #008080;">#180</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/180</span><span class="p">)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit amplicon`</span>:</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"><span class="p"> -</span> fix bug of <span class="sb" style="color: #d14;">`-m`</span>, when mismatch is allowed.</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit fx2tab`</span>:</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"><span class="p"> -</span> new flag <span class="sb" style="color: #d14;">`-C/--base-count`</span> for counting bases. <span class="p">[</span><span class="nv" style="color: #008080;">#183</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/183</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit tab2fx`</span>:</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"><span class="p"> -</span> fix a rare bug. <span class="p">[</span><span class="nv" style="color: #008080;">#197</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/197</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit subseq`</span>:</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"><span class="p"> -</span> fix bug for BED with empty columns. <span class="p">[</span><span class="nv" style="color: #008080;">#195</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/issues/195</span><span class="p">)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit genautocomplete`</span>: </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"><span class="p"> -</span> <span class="gs" style="font-weight: 600;">**support bash|zsh|fish|powershell**</span>.</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
131
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<td class="new_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="markdown"><span class="p">-</span> <span class="p">[</span><span class="nv" style="color: #008080;">SeqKit v0.15.0</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/tag/v0.15.0</span><span class="p">)</span></span>
</pre>
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132
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<td class="new_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Release)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/v0.15.0/total.svg</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)</span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="markdown"><span class="p"> -</span> <span class="sb" style="color: #d14;">`seqkit grep/locate`</span>: update help message.</span>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/74269afe083ed3110d498bcfc78d8652fcde30f8...4bd6a740e922520d8dc9409695075cae1f6aad46#604fd55a896e470ee80f4ea9caf71f879579d68c"><strong>seqkit/cmd/pair.go</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,7 +86,10 @@ Attensions:</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="go"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="go"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">addSuffix</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outdir</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"./"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outdir</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"."</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="go"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filepath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Clean</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Dir</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">filepath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Clean</span><span class="p">(</span><span class="n" style="color: #333;">outdir</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="go"> <span class="n" style="color: #333;">addSuffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outdir</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"./"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">outdir</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"."</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="go"> <span class="n" style="color: #333;">existed</span><span class="p">,</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">pathutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DirExists</span><span class="p">(</span><span class="n" style="color: #333;">outdir</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="go"> <span class="n" style="color: #333;">checkError</span><span class="p">(</span><span class="n" style="color: #333;">err</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">existed</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,8 +106,6 @@ Attensions:</td>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="go"> <span class="n" style="color: #333;">checkError</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MkdirAll</span><span class="p">(</span><span class="n" style="color: #333;">outdir</span><span class="p">,</span> <span class="m" style="color: #099;">0755</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="go"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filepath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Clean</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Dir</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">filepath</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Clean</span><span class="p">(</span><span class="n" style="color: #333;">outdir</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="go"> <span class="n" style="color: #333;">addSuffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="go"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="go"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">reader1</span><span class="p">,</span> <span class="n" style="color: #333;">reader2</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fastx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Reader</span></span>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/74269afe083ed3110d498bcfc78d8652fcde30f8...4bd6a740e922520d8dc9409695075cae1f6aad46#1d415668e438829ee466a5e6b51f9c42ca064b0c"><strong>seqkit/cmd/shuffle.go</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -216,6 +216,9 @@ Secondly, seqkit shuffles sequence IDs and extract sequences by FASTA index.</td>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="go"> <span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">subseqByFaixNotCleaned</span><span class="p">(</span><span class="n" style="color: #333;">faidx</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>
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217
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="go"> <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Write</span><span class="p">([]</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="p">(</span><span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Sprintf</span><span class="p">(</span><span class="s" style="color: #d14;">">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">)))</span></span>
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218
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="go"> <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Write</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="go"> <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WriteString</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="go"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="go"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isStdin</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isPlainFile</span><span class="p">(</span><span class="n" style="color: #333;">file</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">keepTemp</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/74269afe083ed3110d498bcfc78d8652fcde30f8...4bd6a740e922520d8dc9409695075cae1f6aad46#92b5b49951aa33ccf0a6d8b10622240cc64511e8"><strong>seqkit/cmd/sort.go</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -399,8 +399,7 @@ and extracts sequences by FASTA index.</td>
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="go"> <span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">subseqByFaixNotCleaned</span><span class="p">(</span><span class="n" style="color: #333;">faidx</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="go"> <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Write</span><span class="p">([]</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="p">(</span><span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Sprintf</span><span class="p">(</span><span class="s" style="color: #d14;">">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">)))</span></span>
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401
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="go"> <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Write</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="go"> <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WriteString</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="go"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="go"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -416,8 +415,7 @@ and extracts sequences by FASTA index.</td>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="go"> <span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">:=</span> <span class="n" style="color: #333;">subseqByFaixNotCleaned</span><span class="p">(</span><span class="n" style="color: #333;">faidx</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="go"> <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Write</span><span class="p">([]</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="p">(</span><span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Sprintf</span><span class="p">(</span><span class="s" style="color: #d14;">">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">chr</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="go"> <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Write</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="m" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="m" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\n'</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="go"> <span class="n" style="color: #333;">outfh</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">WriteString</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="go"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="go"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/74269afe083ed3110d498bcfc78d8652fcde30f8...4bd6a740e922520d8dc9409695075cae1f6aad46#9b440ae881620aea38a06351cb2ab92f966a94f0"><strong>seqkit/cmd/version.go</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +29,7 @@ import (</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="go"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="go"><span class="c" style="color: #998; font-style: italic;">// VERSION of seqkit</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="go"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.16.<span class="idiff left right">0</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="go"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.16.<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="go"><span class="c" style="color: #998; font-style: italic;">// versionCmd represents the version command</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="go"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">versionCmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cobra</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Command</span><span class="p">{</span></span>
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